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Head-to-head comparison of three experimental methods of quantifying competitive fitness in C. elegans.

ABSTRACT: Organismal fitness is relevant in many contexts in biology. The most meaningful experimental measure of fitness is competitive fitness, when two or more entities (e.g., genotypes) are allowed to compete directly. In theory, competitive fitness is simple to measure: an experimental population is initiated with the different types in known proportions and allowed to evolve under experimental conditions to a predefined endpoint. In practice, there are several obstacles to obtaining robust estimates of competitive fitness in multicellular organisms, the most pervasive of which is simply the time it takes to count many individuals of different types from many replicate populations. Methods by which counting can be automated in high throughput are desirable, but for automated methods to be useful, the bias and technical variance associated with the method must be (a) known, and (b) sufficiently small relative to other sources of bias and variance to make the effort worthwhile. The nematode Caenorhabditis elegans is an important model organism, and the fitness effects of genotype and environmental conditions are often of interest. We report a comparison of three experimental methods of quantifying competitive fitness, in which wild-type strains are competed against GFP-marked competitors under standard laboratory conditions. Population samples were split into three replicates and counted (1) "by eye" from a saved image, (2) from the same image using CellProfiler image analysis software, and (3) with a large particle flow cytometer (a "worm sorter"). From 720 replicate samples, neither the frequency of wild-type worms nor the among-sample variance differed significantly between the three methods. CellProfiler and the worm sorter provide at least a tenfold increase in sample handling speed with little (if any) bias or increase in variance.

SUBMITTER: Crombie TA

PROVIDER: S-EPMC6195253 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Head-to-head comparison of three experimental methods of quantifying competitive fitness in C. elegans.

Crombie Timothy A TA Saber Sayran S Saxena Ayush Shekhar AS Egan Robyn R Baer Charles F CF

PloS one 20181019 10

Organismal fitness is relevant in many contexts in biology. The most meaningful experimental measure of fitness is competitive fitness, when two or more entities (e.g., genotypes) are allowed to compete directly. In theory, competitive fitness is simple to measure: an experimental population is initiated with the different types in known proportions and allowed to evolve under experimental conditions to a predefined endpoint. In practice, there are several obstacles to obtaining robust estimates ...[more]

PMID: 30339672

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Project description:It has been suggested that pathway analysis can complement single-SNP analysis in exploring genomewide association data. Pathway analysis incorporates the available biological knowledge of genes and SNPs and is expected to improve the chances of revealing the underlying genetic architecture of complex traits. Methods for pathway analysis can be classified as competitive (enrichment) or self-contained (association) according to the hypothesis tested. Although association tests are statistically more powerful than enrichment tests they can be difficult to calibrate because biases in analysis accumulate across multiple SNPs or genes. Furthermore, enrichment tests can be more scientifically relevant than association tests, as they detect pathways with relatively more evidence for association than the remaining genes. Here we show how some well known association tests can be simply adapted to test for enrichment, and compare their performance to some established enrichment tests. We propose versions of the Adaptive Rank Truncated Product (ARTP), Tail Strength Measure and Fisher's combination of p-values for testing the enrichment null hypothesis. We compare the behaviour of these proposed methods with the established Hypergeometric Test and Gene-Set Enrichment Analysis (GSEA). The results of the simulation study show that the modified version of the ARTP method has generally the best performance across the situations considered. The methods were also applied for finding enriched pathways for body mass index (BMI) and platelet function phenotypes. The pathway analysis of BMI identified the Vasoactive Intestinal Peptide pathway as significantly associated with BMI. This pathway has been previously reported as associated with BMI and the risk of obesity. The ARTP method was the method that identified the largest number of enriched pathways across all tested pathway databases and phenotypes. The simulation and data application results are in agreement with previous work on association tests and suggests that the ARTP should be preferred for both enrichment and association testing.

Project description:ObjectiveTreatment decisions in inflammatory bowel diseases are increasingly based on longitudinal tracking of calprotectin results. Many hospital laboratories measure calprotectin levels in sent-in stool samples with an enzyme-linked immunosorbent assay (ELISA). Several manufacturers introduced a lateral flow-based test with software application that turns a smartphone camera into a reader for quantitative measurements. We compared three home tests (IBDoc, QuantonCal and CalproSmart) and companion ELISA tests (fCAL, IDK-Calprotectin and Calprotectin-ALP) to see if measurement pairs agreed sufficiently.DesignA method comparison study was conducted with stool samples from patients with active or quiescent inflammatory bowel disease. Medical students without any specific laboratory training carried out the home tests with two iOS (iPhone 6 and 7) and two Android devices (Samsung Galaxy S6 and Motorola Moto G5 Plus). Two experienced laboratory technicians measured the calprotectin concentration with the ELISA method. Primary outcome was test agreement (defined as percentage of paired measurements within predefined limits of difference). Secondary outcome included reading error rate (RER) per smartphone type.ResultsWe performed 1440 smartphone readings and 120 ELISA tests. In the low calprotectin range (≤500 μg/g) IBDoc, QuantOnCal and CalproSmart showed 87%, 82% and 76% agreement with their companion ELISAs. In the high range (>500 μg/g) the agreement was 37%, 19% and 37%, respectively. CalproSmart and QuantOnCal had significantly higher RERs than IBDoc (respectively 5.8% and 4.8%, versus 1.9%). Forty-three percent of reading errors was on the Motorola device, in particular with the QuantOnCal application.ConclusionsAll three calprotectin home tests and companion ELISAs agreed sufficiently when concentrations are ≤500 μg/g. To minimize wrongful interpretation of calprotectin changes over time it is essential to always use the home test and companion ELISA of one and the same manufacturer. Manufacturers should explicitly evaluate and report the suitability of commonly used smartphones for quantitative calprotectin readings.

Dataset Information

Head-to-head comparison of three experimental methods of quantifying competitive fitness in C. elegans.

Publications

Head-to-head comparison of three experimental methods of quantifying competitive fitness in C. elegans.

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